It only appears so. If you compare maps and setups with another player
you will discover that it appears that your home systems are located
in the same hex. This is in fact not the case. Each
race uses its own coordinate system to identify galactic sectors (hexes)
and each race places its home world at the center of the universe. So e.g. in a
galaxy of size 28 columns by 28 rows, all races will use the hex number H1414
to refer to their home system, even though in fact all home systems are
in different hexes.
If two players want to find out where they are really located
relative to each other, they must find some common reference. When the
two players encounter each other, they can of course use the hex of the
encounter as a reference. Before an actual encounter they have only
the pattern of star systems, black holes and dust clouds on their maps
to go by - they may be able to identify an area where their maps
overlap. At the start of the game your map will actually only overlap
with maps of neighbouring races, so it is quite impossible
for two players to find out what their relative locations are unless
they start out as neighbours.

No, a colony transport or exodus ship can only unload population to a
colony with the colonize order, after which it is dismantled.
Only a stasis transport can load and unload population and
thus be re-used.